R-loops are formed over expanded repeats of <i>FXN</i> gene in FRDA cells.

<p>A. Diagram of <i>FXN</i> gene. Black boxes are exons, white boxes are 5′ and 3′UTRs, lines are introns, red triangle is (GAA)_n expansion. TSS2 is the major transcriptional start site in lymphoblastoid cells. qPCR amplicons are shown below the diagram. Numbers indicate the distances to TSS2 in kilobases. B. Cell lines used in the study. The repeat sizes are indicated. C. RT-qPCR analysis of γ-actin, β-actin, GAPDH and <i>FXN</i> mRNAs in control (GM15851) and FRDA (GM15850) cells. Values are normalised to 5S rRNA and relative to control cells. D. RNA Pol II ChIP in control (GM15851) and FRDA (GM15850) cells. E. RT-qPCR analysis of <i>FXN</i> nascent RNA in control (GM15851) and FRDA (GM15850) cells, normalised to 5S rRNA and relative to ex1 RNA in control cells. F. DIP on endogenous <i>FXN</i> gene in control (GM15851) and FRDA (GM15851) cells. γ-actin is positive control. G. R-loops are sensitive to RNase H digestion. DIP samples were treated with 25 U of recombinant <i>E.coli</i> RNase H (NEB, M0297S) for 6 hours at 37°C. γ-actin is positive control. Bars in C–G are average values +/− SEM (n>3).</p

R-loops are stable and impede Pol II transcription on <i>FXN</i> gene.

<p>A. RT-qPCR analysis of nascent γ-actin and <i>FXN</i> RNA from control and FRDA cells treated with 5 µg/ml of actinomycin D for 21 hours. Values are relative to untreated control cells. B. DIP on <i>FXN</i> gene in control and FRDA cells treated with 5 µg/ml of actinomycin D for 21 hours. γ-actin is positive control. C. H3K9me2 ChIP in control and FRDA cells. H3K9me2 levels were normalized to the total H3 levels. γ-actin is used as background control. D. Diagram depicting the Br-UTP nuclear run-on (NRO) method. E. Br-UTP nuclear run-on in two control (GM15851, GM14926) and two FRDA (GM15850 and GM16243) cells, normalised to the region B in control cells. Bars in A–C and E are average values +/− SEM (n>3).</p

Over-expressed RNase H1 resolves R-loops formed on <i>FXN</i> expanded repeats in HEK293 cells.

<p>A. Diagram of the FXN-Luc gene, containing 6 (<i>FXN-Luc</i>) or 310 GAA repeats (<i>FXN-GAA-Luc</i>), integrated on the chromosome 1 of HEK293 cells. Frataxin gene was fused to the luciferase at the beginning of the <i>FXN</i> exon 5. Black boxes are exons, white boxes are 5′ and 3′UTRs, lines are introns, red triangle is (GAA)_n expansion. TSS is the transcriptional start site. qPCR amplicons are shown below the diagram. Numbers indicate the distances to TSS in kilobases. B. Size of GAA expansion determined by PCR analysis on genomic DNA from <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> cell lines, using GAA104F and GAA629R primers. PCR products were run on 1% agarose gel. M denotes the marker lane. <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> cells contain endogenous wild type <i>FXN</i> gene <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004318#pgen.1004318-Lufino1" target="_blank">[23]</a>, giving rise to the PCR product of 0.5 kb. C. <i>FXN</i> and γ-actin nascent RNA levels in <i>FXN-Luc</i> (white bars) and <i>FXN-GAA-Luc</i> (black bars) HEK293 cells, determined by RT-qPCR and normalised to 5S rRNA. The level of <i>FXN</i> and γ-actin nascent RNA in <i>FXN-Luc</i> cells was taken as 1. LucR primer was used for the reverse transcription reaction. qPCR was carried using in4F and ex5R primers, shown in A. D. DIP analysis on <i>FXN-Luc</i> gene in <i>FXN-Luc</i> (white bars) and <i>FXN-GAA-Luc</i> (black bars) HEK293 cells using RNA/DNA hybrid-specific S9.6 antibody. E. RT-qPCR analysis of RNase H1 mRNA from <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> cells, treated with control and RNase H1 siRNAs. Values are normalised to GAPDH mRNA and are relative to <i>FXN-Luc</i> cells, treated with control siRNA. F. DIP analysis on <i>FXN-Luc</i> gene in <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> HEK293 cells, treated with control and RNase H1 siRNAs. G. Western blot analysis of 50 µg of protein extracts obtained from <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> cells transfected with Flag and RNase H1-Flag expression plasmids. Western blot was probed with anti-RNase H1 antibody. * denotes endogenous RNase H1 protein. H. DIP analysis on <i>FXN-Luc</i> gene in <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> HEK293 cells transfected with Flag or RNase H1-Flag expression plasmids. Bars in C–F and H represent the average values from at least three independent experiments +/− SEM.</p

R-loops trigger transcriptional repression of <i>FXN</i> gene.

<p>A. DIP analysis on <i>FXN</i> gene in control and FRDA cells, treated with 10 µM camptothecin (CPT) for 6 hours. B. H3K9me2 ChIP on <i>FXN</i> gene in control and FRDA cells, treated with 10 µM camptothecin (CPT) for 6 hours. H3K9me2 levels were normalized to the total H3 levels. C. RT-qPCR analysis of <i>FXN</i> nascent RNA in control and FRDA cells, treated with 10 µM camptothecin for 6 hours. Values are relative to untreated control cells and normalized to γ-actin nascent RNA. D. G9a ChIP on <i>FXN</i> gene in control and FRDA cells. G9a levels are normalised relative to amplicon B in control cells. E. Western blot analysis of 20 and 40 µg of protein extracts obtained from <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> cells, treated with control and Top1 siRNAs. Western blot was probed with anti-Top1 and anti-actin antibody. F. DIP analysis on <i>FXN</i> gene in <i>FXN-Luc</i> and <i>FXN-GAA-Luc</i> HEK293 cells, treated with control and Top1 siRNAs. Bars in A–D and F are average values +/− SEM (n>3).</p

R-loops are not affected by changes in H3K9 dimethylation.

<p>A. H3K9me2 ChIP in control and FRDA cells, treated with 4 µM BIX-01294 for 72 h. H3K9me2 levels were normalized to the total H3 levels and relative to amplicon <i>FXN</i> A, not affected by the treatment. B. DIP analysis in control and FRDA cells, treated with 4 µM BIX-01294 for 72 h. C. RT-qPCR analysis of <i>FXN</i> nascent RNA in control and FRDA cells, treated with 4 µM BIX-01294 for 72 h. Values are relative to untreated control cells and normalized to γ-actin nascent RNA. Bars in A–C are average values +/− SEM (n>3).</p

R-loops are formed over (CGG)_n expanded repeats of <i>FMR1</i> gene.

<p>A. Diagram of <i>FMR1</i> gene. Black boxes are exons, white box is 5′ UTR and lines are introns. Red triangle is (CGG)_n expansion. qPCR amplicons are shown below the diagram. TSS is the transcriptional start site. Numbers indicate the distances to TSS in kilobases. B. RT-qPCR analysis of <i>FMR1</i> mRNA in control and FXS cells, treated with 1 µM 5-azadC for 7 days, normalized to GAPDH. C. DIP analysis on endogenous <i>FMR1</i> gene in control and FXS cells, treated with 1 µM 5-azadC for 7 days. Values are relative to ex1 region in control untreated cells. D. <i>FMR1</i> R-loops are sensitive to RNase H digestion, following the treatment with 25 U of RNase H for 6 hours at 37°C prior to immuno-precipitation. Values are relative to in15 region in control untreated cells. E. R-loop kinetics on exon 1 of <i>FMR1</i> gene in control and FXS cells during the process of transcriptional re-activation with 1 µM 5-azadC (7 days) followed by 5-azadC wash out with drug-free media (28 days). Values are relative to ex1 region in control untreated cells on day 7. F. RT-qPCR analysis of <i>FMR1</i> mRNA in control and FXS cells, treated with 1 µM 5-azadC (7 days) followed by 5-azadC wash out with drug-free media (28 days). The level of <i>FMR1</i> mRNA in control cells is taken as 1. Bars in B–D are average values +/− SEM (n>3).</p

Model for the role of R-loops in mediating <i>FXN</i> and <i>FMR1</i> gene silencing.

<p>Background R-loop level on wild type allele allows efficient transcriptional elongation and gene expression. Transcribed (GAA)_n and (CGG)_n expanded repeats form R-loops resulting in decreased initiation and elongation of RNA Pol II. This leads to downregulation of <i>FXN</i> and <i>FMR1</i> expression, associated with formation of repressive DNA and chromatin marks.</p